Modelling Compounds and Molecules


 

If you were to look at water, you wouldn't be able to tell it's composed of hydrogen and oxygen atoms in the ratio of 2:1. Unless you used a really good microscope, that is, but let's assume you didn't, and instead you stood there, contemplating what it's made out of. 

Eventually, you get bored of this and look up what the chemical formula of water is - it's H2O. Now you have your answer, an answer which has only been known since the 1800s. With your new-found knowledge, you'd like to show everyone what a water molecule looks like. Here are some methods you could use, ranging from the artistic to the minimalist (but not every method necessarily works with water).

The Ball and Stick Model

Ball and stick model of water

You have the individual atoms, which are balls, and the bonds between them (in the case of water, intermolecular forces, as in hydrogen bonds) are sticks. This is a 3D model, representing the sizes of each of the atoms (notice how the solitary oxygen atom is much larger than the hydrogen atoms), and you can see that the atoms are at an angle to each other around the central atom.

It's not a particularly elegant way to depict a molecule in my opinion - sure, it does a good job, but it doesn't look as nice as some other molecular models. Most importantly, the distances between the atoms are very distorted - it's about 96 pm between the oxygen atom and a hydrogen atom, yet you wouldn't assume that when looking at the stick. Yes, you could label the length, but a model shouldn't have to do that - you should be able to interpret this fact from looking at it.

So the next solution is to snap the sticks in half - this is where the space filling model comes in. The atoms are still proportional to their size, but so are the distances between the atoms:

Space filling model of water

Much like the ball and stick model, this shows the molecule as a 3D object, but unlike a ball and stick model, these are more grounded in reality - you can compare the sizes of these molecules more easily because there are no sticks getting in the way - a sulphur atom is much larger than an oxygen atom, so as you'd expect, an H2S molecule looks larger than an H2O molecule.  

In both of these examples, you may wonder why the oxygen atom is red and the hydrogen atoms are white. This is due to a colour scheme known as the CPK colour values, which also dictate carbon to be grey, amongst other various colours. This website's got you sorted if you're interested in that sort of thing.

Focusing on space filling models, you'll notice that now it's rather difficult to see the angle between the atoms - what you gained in physical reality, you lost in geometric ease. So you need to get more simplified (which in a way is the best thing with models - you're not trying to be completely accurate, rather show what something should be).

Enter the Lewis structure:

Lewis structure model of water 

This is a rather crude version that I made in Microsoft Paint of a water molecule. This one isn't as good as the previous two in indicating how big a molecule is or how big it is compared to other molecules, but where it wins out is its practicality. You don't need computer software or plastic components to create this model, and you can also depict how many electrons are not shared in a covalently bonded molecules (in this case, four - two lone pairs). You can also include the distance between various atoms and the dipoles present in the molecule, whilst you don't need to follow colour schemes to know which atoms are bonded. It's almost the classic chemistry model, and for me is the most elegant and useful.

Water is a straight-forward example because there are only single bonds between all the atoms (so only one pair of electrons are shared between atoms in covalent bonds). Should you have double bonds, like in carbon dioxide, you'd have two lines connecting each atom, like this:

Lewis structure model of carbon dioxide 

The same with triple bonds - three lines. This is similar to how the bonds would be represented in ball and stick diagrams - one stick is one bond. 

You can expand upon this to take a 3D perspective, with bolded and striped lines helping to preserve the bonds of the molecule, as in this model of methane.

Element symbols are also used in dot and cross diagrams, a popular model for ionic bonds. Here's an example with calcium oxide:

Dot and cross diagram of calcium oxide 

This one involves the outer shell electrons only, in accordance with the Bohr model of the atom. As can be seen here, for every calcium ion, there is one oxide ion - the calcium atom donates two electrons to each oxygen atom for both to be ionised (as per the crosses - these are the calcium electrons). You could show how big these ions are compared to each other, but you wouldn't be able to compare their sizes. 

As time has gone on, each model has become more and more simplified, going from unrealistic 3D to pictorial 2D. It would thus make sense for something like skeletal diagrams to be used, which focus primarily on the present bonds. As the name suggests, they are very simplified:

Skeletal diagram of cyclohexane - or is it just a hexagon? 

This is a hexagon - or cyclohexane. It's chemical formula is C6H12, but you may not be able to assume that from the model. Each carbon atom must bond to four other atoms - in the case of cyclohexane, that will be two adjacent carbon atoms, as well as to two hydrogen molecules - hence the hexagon shape. Double bonds will obviously be represented with two lines, as in the case with benzene.

Skeletal diagrams would be more useful if you've got a very large molecule, consisting of countless atoms all bonded to each other - so by simplifying the molecule down to its carbon bonds and only showing the non-carbon and hydrogen atoms, you can save a lot of space, time and ink. It's also somewhat nice geometrically, conserving the angles between bonds (the shape of cyclohexane might convince you one bonding angle is 120°, but it's actually 109.5° - but all the angles are of an equal size at least).

Cyclohexane might look like a hexagon, but that's only from one angle. It looks like a discarded crisp packet in its chair conformation (one of the shapes cyclohexane takes) for example. 

And all you wanted to know is what water is composed of...

All diagrams were made by me in Paint - barring the first two, which were taken from the Wikipedia article on water - the link to the article is here, and you can find the diagrams at the top of the infobox.

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